Carefully read the terms and conditions.
They don't recommend travel/trip insurance for no reason.
If everything goes sideways on your trip, refer back to step one.
Aggressor fleet is the largest liveaboard operator in the world. They hire great captains and crew, and they have excellent vessels. With that said, there is always a chance of having a musty smelling cabin, or the shower drain is clogged, or the A/C drips on your bunk. If there is an issue, let the Captain/Engineer know. They are there to prevent you from complaining by fixing your stuff.
Do not try to negotiate the terms and conditions from step 1. Do not change the liability release. Do not lie on the medical. All of those documents are to protect the dive operator and are non-negotiable.
You will have a chef on the boat. If you say you are gluten free, the chef will prepare gluten free meals for you. Do not rile the chef by having the brownies after the night dive. It will be noticed by the crew and they will gossip about you behind your back. They won't be discreet and they don't care if you know or hear them. They bent over backwards to accommodate you and you just crapped in their fruit-loops.
The crew on an aggressor will take care of you as much as you need or desire. One DM will be in the water for about 45 minutes on every dive. You may stick with the DM or you and your buddy may go off on your own. The guide is coming back early to help you board and fill your cylinders. You may choose to return to the vessel with the guide.
You must bring a buddy or one will be assigned. An assigned buddy may not be to your (either of your) liking.
As far as liveaboard.com or booking directly, Aggressor has a reputation of not talking to the customer aside from taking your money, providing needed information, and hassling you when signed documents aren't returned on time. If your trip does go sideways, you will have no communications and no recourse. At least using a booking agent, you're paying them to be nice to you, advocate for you, and someone to get you out of the weeds if revolution happens while you're offshore. A good travel agent is worth their weight in gold when you need them.
Finally are there any other Roatan options out there?
I would never bother with a liveaboard in Roatan. I'd do Coco-View or AKR every time.